The US has confirmed it is flying armed drones in Iraq. Photograph: Sipa Press/Rex Features

The US has confirmed it is flying armed drones over Baghdad to protect US troops who recently arrived to assess Iraq's deteriorating security.

The military for more than a week has been flying manned and unmanned aircraft over Iraq, averaging a few dozen sorties daily for reconnaissance, according to the Pentagon. The decision to arm some of the drones follows the deployment to Baghdad of troops whose publicly stated role is to advise and assist Iraqi forces fighting Isis militants who have seized a number of cities and key facilities.

"The reason that some of those aircraft are armed is primarily for force protection reasons now that we have introduced into the country some military advisers whose objective will be to operate outside the confines of the embassy," said the defence department's press secretary, Navy Rear Admiral John Kirby.

A handful of Predators armed with Hellfire missiles were being used over the capital for the new force protection mission, a senior defence official said. The official was not authorised to discuss the new flights on the record and requested anonymity.

Officials stressed that Obama still had not authorised air strikes against Sunni militants who have been overrunning territory in other parts of the country.

Sending aircraft to target the leaders of the Sunni-led insurgency was one of the options being prepared for President Barack Obama as he considered what support to provide to Iraq, the chairman of the joint chiefs of staff, General Martin Dempsey, said in a radio interview. Protection of critical infrastructure was part of that option, he said.

"We're flying a great deal [of] manned and unmanned ... intelligence and reconnaissance assets, and we're building a picture so that if the decision were made to support the Iraqi security forces as they confront (Isis) we could do so," Dempsey said.

So far 180 of 300 troops promised by Obama have arrived in the country. The contingent includes 90 advisers and 90 who are setting up an operations and intelligence analysis unit.